The major focus of the research proposed is to understand the biological roles of sequences that have potential to adopt non-B DNA structures when subjected to superhelical strain (non-B sequences). These sequences are specifically recognized and reacted by chemical carcinogens with different reaction specificities when they are forming non-B DNA structures in supercoiled plasmid DNA. Our recent work strongly suggested that certain non-B sequences can modulate gene expression through non-B DNA structure intermediates. We also cloned a human cDNA that encodes a protein (SATB1) that specifically recognizes special AT-rich sequences that become stably base-unpaired under superhelical strain. We found that nuclear matrix associating DNAs (MARs) have this structural property and bind to SATB1. Thus, studies on the biological significance of non-B sequences facilitate understanding of regulation in gene expression and simultaneously provide the molecular basis to understand how chemical carcinogens cause cancer. In this grant application, we propose to study the biological roles of the non-B sequences recognized by SATB1. In particular, we will examine whether these elements can act as boundary sequences which confer an independent gene activity of a linked gene in vivo. We will also examine whether these non-B sequences are preferential targets for chemical carcinogen reactions in vivo. Possible structural effects on DNA by SATB1 binding will be studied. By employing the tissue culture system, as well as the targeted gene inactivation in the mouse germ line, we will study the biological function of SATB1 protein.